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- PDB-7ig2: Endothiapepsin crystal Apo07 from ECBL-96 fragment library screen... -

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Basic information

Entry
Database: PDB / ID: 7ig2
TitleEndothiapepsin crystal Apo07 from ECBL-96 fragment library screening campaign used for PanDDA ground state calculation
ComponentsEndothiapepsin
KeywordsHYDROLASE / crystallographic fragment screening / Endothiapepsin / ECBL-96 fragment library
Function / homology
Function and homology information


endothiapepsin / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsWollenhaupt, J. / Benz, L.S. / Jirgensons, A. / Miletic, T. / Mueller, U. / Weiss, M.S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission871037European Union
CitationJournal: Rsc Med Chem / Year: 2025
Title: From fragments to follow-ups: rapid hit expansion by making use of EU-OPENSCREEN resources.
Authors: Benz, L.S. / Wollenhaupt, J. / Jirgensons, A. / Miletic, T. / Mueller, U. / Weiss, M.S.
History
DepositionJun 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endothiapepsin


Theoretical massNumber of molelcules
Total (without water)33,8141
Polymers33,8141
Non-polymers00
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.350, 73.140, 52.640
Angle α, β, γ (deg.)90.00, 109.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endothiapepsin / Aspartate protease


Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 29 % (w/v) PEG 4000, 0.1 M ammonium acetate and 0.1 M sodium acetate, pH 4.6
Time: 2-3 days

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.07→36.57 Å / Num. obs: 139407 / % possible obs: 97.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.093 / Net I/σ(I): 7.42 / Num. measured all: 460334
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
1.07-1.1395.31.33566370219580.3491.6270.71
1.13-1.2197.90.80767980211200.5690.9721.28
1.21-1.3197.20.61862978195770.6880.7421.7
1.31-1.4399.30.38263180184010.8590.4552.88
1.43-1.697.90.20854760164090.9550.2485.16
1.6-1.8599.20.11151809147120.9870.1319.87
1.85-2.2797.60.05740916122650.9950.06918.6
2.27-3.2990.0393433596420.9970.04727.28

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Processing

Software
NameVersionClassification
PHENIX(1.17_3644: ???)refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→36.57 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1697 2099 1.51 %
Rwork0.1492 --
obs0.1495 139395 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.07→36.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 0 325 2694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052536
X-RAY DIFFRACTIONf_angle_d0.8773505
X-RAY DIFFRACTIONf_dihedral_angle_d17.586844
X-RAY DIFFRACTIONf_chiral_restr0.075420
X-RAY DIFFRACTIONf_plane_restr0.006452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.090.34241370.3368958X-RAY DIFFRACTION96
1.09-1.120.31171370.29788955X-RAY DIFFRACTION96
1.12-1.150.27881340.27678793X-RAY DIFFRACTION95
1.15-1.190.22851420.24549251X-RAY DIFFRACTION99
1.19-1.220.23051400.22459192X-RAY DIFFRACTION98
1.22-1.270.25361400.21429135X-RAY DIFFRACTION98
1.27-1.320.25561380.19879016X-RAY DIFFRACTION96
1.32-1.380.191420.17099270X-RAY DIFFRACTION99
1.38-1.450.17251410.14929266X-RAY DIFFRACTION99
1.45-1.540.17361410.12729205X-RAY DIFFRACTION99
1.54-1.660.1581400.1169143X-RAY DIFFRACTION98
1.66-1.830.12521420.10649296X-RAY DIFFRACTION99
1.83-2.090.13081420.10559269X-RAY DIFFRACTION99
2.09-2.640.12641400.12019182X-RAY DIFFRACTION98
2.64-36.570.16331430.14349365X-RAY DIFFRACTION99

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